Identification of Immune Genes of the Agamaki Clam (Sinonovacula constricta) by Sequencing and Bioinformatic Analysis of ESTs
The Agamaki clam (Sinonovacula constricta) is an economically important shellfish in Asia. However, genomic research on this species is still in its infancy, and genomic resources are largely unavailable. The objective of this study was to generate expressed sequence tags (ESTs) from a normalized li...
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| Veröffentlicht in: | Marine biotechnology (New York, N.Y.) N.Y.), 2010-06, Vol.12 (3), p.282-291 |
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| creator | Feng, Bingbing Dong, Lingli Niu, Donghong Meng, Shanshan Zhang, Bing Liu, Dabo Hu, Songnian Li, Jiale |
| description | The Agamaki clam (Sinonovacula constricta) is an economically important shellfish in Asia. However, genomic research on this species is still in its infancy, and genomic resources are largely unavailable. The objective of this study was to generate expressed sequence tags (ESTs) from a normalized liver complementary DNA library and to identify genes that function in immune defense. A total of 5,296 ESTs were sequenced, from which 540 contigs and 3,473 singletons were identified. BLAST homology analysis indicated that only 20.7% of these ESTs were homologues of known genes while the remaining 79.3% appeared to be novel sequences. Based on sequence similarities, 43 putative immune genes were identified that encode proteases and protease inhibitors, adhesive proteins, stress proteins, lysosomal enzymes, and signal transduction regulators. Our study thus provides both a large collection of novel transcripts and a detailed annotation of immune genes for an important bivalve species. |
| doi_str_mv | 10.1007/s10126-009-9216-z |
| format | Article |
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However, genomic research on this species is still in its infancy, and genomic resources are largely unavailable. The objective of this study was to generate expressed sequence tags (ESTs) from a normalized liver complementary DNA library and to identify genes that function in immune defense. A total of 5,296 ESTs were sequenced, from which 540 contigs and 3,473 singletons were identified. BLAST homology analysis indicated that only 20.7% of these ESTs were homologues of known genes while the remaining 79.3% appeared to be novel sequences. Based on sequence similarities, 43 putative immune genes were identified that encode proteases and protease inhibitors, adhesive proteins, stress proteins, lysosomal enzymes, and signal transduction regulators. Our study thus provides both a large collection of novel transcripts and a detailed annotation of immune genes for an important bivalve species.</description><identifier>ISSN: 1436-2228</identifier><identifier>EISSN: 1436-2236</identifier><identifier>DOI: 10.1007/s10126-009-9216-z</identifier><identifier>PMID: 19590922</identifier><language>eng</language><publisher>New York: New York : Springer-Verlag</publisher><subject>Animals ; Aquaculture ; bioinformatics ; Biomedical and Life Sciences ; Biotechnology ; Bivalvia ; Bivalvia - genetics ; Bivalvia - immunology ; cDNA libraries ; cDNA library ; clams ; Cloning ; Computational Biology ; Computational Biology - methods ; Economic importance ; Engineering ; Enzymes ; Expressed Sequence Tags ; Expressed sequence tags (ESTs) ; Freshwater & Marine Ecology ; Gene expression ; Gene Expression Profiling ; Genes ; genetics ; Genomes ; Genomics ; Immune gene ; immunology ; Laboratories ; Life Sciences ; Liver ; Marine ; Marine biology ; methods ; Microbiology ; Molecular Sequence Data ; Mollusks ; Original Article ; Proteinase inhibitors ; Proteins ; Shellfish ; Signal transduction ; Sinonovacula constricta ; Studies ; Zoology</subject><ispartof>Marine biotechnology (New York, N.Y.), 2010-06, Vol.12 (3), p.282-291</ispartof><rights>Springer Science+Business Media, LLC 2009</rights><rights>Springer Science+Business Media, LLC 2010</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c524t-c32a8e741385ec0dcdbba5133e1bddf3906a8fe914bbb3e4f12ac377567717c43</citedby><cites>FETCH-LOGICAL-c524t-c32a8e741385ec0dcdbba5133e1bddf3906a8fe914bbb3e4f12ac377567717c43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10126-009-9216-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10126-009-9216-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19590922$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Feng, Bingbing</creatorcontrib><creatorcontrib>Dong, Lingli</creatorcontrib><creatorcontrib>Niu, Donghong</creatorcontrib><creatorcontrib>Meng, Shanshan</creatorcontrib><creatorcontrib>Zhang, Bing</creatorcontrib><creatorcontrib>Liu, Dabo</creatorcontrib><creatorcontrib>Hu, Songnian</creatorcontrib><creatorcontrib>Li, Jiale</creatorcontrib><title>Identification of Immune Genes of the Agamaki Clam (Sinonovacula constricta) by Sequencing and Bioinformatic Analysis of ESTs</title><title>Marine biotechnology (New York, N.Y.)</title><addtitle>Mar Biotechnol</addtitle><addtitle>Mar Biotechnol (NY)</addtitle><description>The Agamaki clam (Sinonovacula constricta) is an economically important shellfish in Asia. However, genomic research on this species is still in its infancy, and genomic resources are largely unavailable. The objective of this study was to generate expressed sequence tags (ESTs) from a normalized liver complementary DNA library and to identify genes that function in immune defense. A total of 5,296 ESTs were sequenced, from which 540 contigs and 3,473 singletons were identified. BLAST homology analysis indicated that only 20.7% of these ESTs were homologues of known genes while the remaining 79.3% appeared to be novel sequences. Based on sequence similarities, 43 putative immune genes were identified that encode proteases and protease inhibitors, adhesive proteins, stress proteins, lysosomal enzymes, and signal transduction regulators. Our study thus provides both a large collection of novel transcripts and a detailed annotation of immune genes for an important bivalve species.</description><subject>Animals</subject><subject>Aquaculture</subject><subject>bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Bivalvia</subject><subject>Bivalvia - genetics</subject><subject>Bivalvia - immunology</subject><subject>cDNA libraries</subject><subject>cDNA library</subject><subject>clams</subject><subject>Cloning</subject><subject>Computational Biology</subject><subject>Computational Biology - methods</subject><subject>Economic importance</subject><subject>Engineering</subject><subject>Enzymes</subject><subject>Expressed Sequence Tags</subject><subject>Expressed sequence tags (ESTs)</subject><subject>Freshwater & Marine Ecology</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Genes</subject><subject>genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Immune gene</subject><subject>immunology</subject><subject>Laboratories</subject><subject>Life Sciences</subject><subject>Liver</subject><subject>Marine</subject><subject>Marine biology</subject><subject>methods</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Mollusks</subject><subject>Original Article</subject><subject>Proteinase inhibitors</subject><subject>Proteins</subject><subject>Shellfish</subject><subject>Signal transduction</subject><subject>Sinonovacula 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| subjects | Animals Aquaculture bioinformatics Biomedical and Life Sciences Biotechnology Bivalvia Bivalvia - genetics Bivalvia - immunology cDNA libraries cDNA library clams Cloning Computational Biology Computational Biology - methods Economic importance Engineering Enzymes Expressed Sequence Tags Expressed sequence tags (ESTs) Freshwater & Marine Ecology Gene expression Gene Expression Profiling Genes genetics Genomes Genomics Immune gene immunology Laboratories Life Sciences Liver Marine Marine biology methods Microbiology Molecular Sequence Data Mollusks Original Article Proteinase inhibitors Proteins Shellfish Signal transduction Sinonovacula constricta Studies Zoology |
| title | Identification of Immune Genes of the Agamaki Clam (Sinonovacula constricta) by Sequencing and Bioinformatic Analysis of ESTs |
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